Outside the theater lies Glipforg, a vibrant town on Planet 51, where little green aliens lead lives reminiscent of the 1950s in America. Among them is Lem (Justin Long), a teenage alien thrilled to start his new job at the planetarium museum. His best friend Skiff (Seann William Scott), a devoted fan of the "Humaniacs" movie series and owner of the local comic book store, eagerly supports Lem.
As Lem arrives home, he curiously inquires about Neera (Jessica Biel), his long-time crush living next door. The atmosphere is bustling with excitement as Lem's family hosts a barbecue with the neighbors, including Neera. However, his attempts to ask her out are constantly interrupted by her free-spirited friend Glar (Alan Marriott).
Simultaneously, a mysterious spacecraft orbits Planet 51, sending out a blinking red signal. Below, hidden at the secretive Base 9—the alien version of Area 51—an array of earthly artifacts lies in wait. One item comes to life in response to the signal: a wheeled probe named Rover with artificial intelligence. Rover escapes with a singular directive: to find the astronaut and collect rocks. The army soon grows suspicious of its sudden activity.
Just as the barbecue kicks off, a spacecraft lands unexpectedly in Lem's backyard, from which Charles 'Chuck' Baker (Dwayne Johnson), a NASA astronaut, emerges. Startled by an alien "rubber ducky" left on the ground, Chuck tries to return to his lunar module but is quickly blocked by the excited Eckle, who is desperate for an autograph. The shock of discovering an inhabited world sends Chuck into a panic, prompting him to seek refuge while the army mobilizes to investigate.
General Grawl (Gary Oldman) leads the army's efforts against the supposed alien threat, enlisting Professor Kipple (John Cleese) for insights on this extraterrestrial intruder. As they quarantine the area, Lem discovers Chuck hiding at the planetarium. To both their amazement, they find they comprehend one another's language. Realizing Chuck poses no threat, Lem decides to assist him, a choice that costs him his job and nearly lands him in jail.
As the adventure unfolds, Rover locates Chuck, and they share a joyous reunion. Chuck expresses his admiration for Lem's bravery, revealing that it is Lem who embodies "the right stuff," what it means to take risks and make sacrifices. The next day, as the military shifts Chuck’s module away to a top-secret location, Lem and Skiff feel lost when trying to figure out how to help Chuck return to his spacecraft. Inspiration strikes when they learn of a Humaniacs movie premiere featuring a costume contest.
The trio dresses as fans and enters the contest, with Chuck unexpectedly drawing attention. He even introduces a dance to the event, but when Rover crashes the party, chaos erupts. Intrigued by the commotion, General Grawl aliens rush in, and Chuck's American insignia exposes him, resulting in his capture alongside Rover. Lem, now branded a hero, finds himself despairing about Chuck's fate.
Inside Base 9, General Grawl interrogates Chuck under a dire ultimatum as Professor Kipple prepares for a brain dissection. However, Lem's unyielding spirit sees him hotwiring a car to rescue Chuck. Accompanied by Neera and their friends, they begin their daring mission, rallying to find the astronaut and ambounding into a physics-defying journey that reveals their camaraderie.
Through clever teamwork, they manage to infiltrate Base 9, where they free Chuck just as alarms resonate throughout the facility. Their escape leads them to Chuck's lunar module, but when confronted by General Grawl, Lem uses a diversion to allow Chuck and the group to flee to safety. As they hurtle back into orbit, they experience weightlessness together, with Grawl beginning to comprehend Chuck's true nature.
Finally, Chuck descends back to the planet's surface, and despite initial wariness from the army, General Grawl declares him an ally. The aliens of Planet 51 witness the truth of Chuck's harmlessness, and Lem finally builds the courage to ask Neera out. As Chuck prepares to depart, Rover decides to stay, becoming Skiff's new companion.
Even after the credits roll, Professor Kipple, believed to have perished, rises to confront two soldiers who once met Chuck and Rover. As Chuck leaves Planet 51 behind, he finds a surprising stowaway in Rover, who becomes his unexpected pet for the journey ahead.
